file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 41.0 42.0 43.0 43.4 45.0 45.0
## [1] 40
## [1] 41 41 41 42 42 42 42 42 42 42 42 43 43 43 43 43 43 43 43 43 43 43 44 44 44
## [26] 44 44 44 45 45 45 45 45 45 45 45 45 45 45 45
bioMart.All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]alias2Symbol function from
limma.a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"
##
## FALSE TRUE
## 1643 357
##
## FALSE TRUE <NA>
## 21 1622 357
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: BTBD11 ABTB3
## 2: LINC01006 RNF32-DT
## 3: LINC01185 REL-DT
## 4: ZRANB2-AS2 ZRANB2-DT
## 5: LINC00271 AHI1-DT
## 6: RFX3-AS1 RFX3-DT
## 7: COX10-AS1 COX10-DT
## 8: SUCLG2-AS1 SUCLG2-DT
## 9: C5orf17 LINC02899
## 10: OSMR-AS1 OSMR-DT
## 11: C8orf37-AS1 CFAP418-AS1
## 12: CTB-178M22.2 TENM2-AS1
## 13: LINC00637 PPP1R13B-DT
## 14: MPP6 MPHOSPH6
## 15: C7orf61 SPACDR
## 16: C3orf35 APRG1
## 17: HRAT92 PDGFA-DT
## 18: LINC00884 ATP13A3-DT
## 19: LINC01137 ZC3H12A-DT
## 20: TMEM161B-AS1 TMEM161B-DT
## 21: MAFG-DT MILIP
## sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CD38 CD38 CD38
## 2: PRKAR2B PRKAR2B PRKAR2B
## 3: ASB4 ASB4 ASB4
## 4: USH1C USH1C USH1C
## 5: ARHGAP44 ARHGAP44 ARHGAP44
## t1
## 1
## 2000
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp"
## reactome go_bp
## 1692 7647
Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CD38 CD38 CD38
## 2: PRKAR2B PRKAR2B PRKAR2B
## [1] 36517 9
## gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003 FALSE TSPAN6 NCBITaxon:9606
## 2: ENSG00000000005 FALSE TNMD NCBITaxon:9606
## feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1: gene 6900 0.118699020 90.14412
## 2: gene 161 0.002485395 99.77003
## total_counts
## 1: 8310
## 2: 174
## [1] 2000
##
## TRUE
## 2000
##
## FALSE TRUE
## 34517 2000
gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1
table(gene_dat$selected)##
## 0 1
## 34517 2000
## $`0`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00857 90.44551 99.20296 90.72478 99.93429 100.00000
##
## $`1`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 60.04 81.87 72.81 92.88 97.99
gene_info = merge(gene_info, gene_dat, by.x="sym_in_data",
by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)## [1] 2000 12
## sym_in_data sym_limma gene_symbol gene_ids feature_is_filtered
## 1: A2M A2M A2M ENSG00000175899 FALSE
## 2: A2ML1-AS1 A2ML1-AS1 A2ML1-AS1 ENSG00000256661 FALSE
## feature_reference feature_biotype n_cells_by_counts mean_counts
## 1: NCBITaxon:9606 gene 5826 0.1207987
## 2: NCBITaxon:9606 gene 11030 0.2138297
## pct_dropout_by_counts total_counts selected
## 1: 91.67821 8457 1
## 2: 84.24488 14970 1
max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol",
bias.data = 100 - gene_info$pct_dropout_by_counts)
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=81)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "GPNMB" "RNF165" "ARHGAP27" "CCDC141"
## [5] "AGBL2" "ZCCHC18" "RAB39A" "SP140L"
## [9] "WNT7B" "RP1-15D23.2" "CCDC192" "BAALC-AS2"
## [13] "LINC02196" "LINC02745" "KCNG1" "RASGRP2"
## [17] "ARHGAP15" "ANGPT2" "PCDH11Y" "CACNA1I"
## [21] "TNNT2" "HS3ST2" "SLC6A6" "SRRM4"
## [25] "KCNH5" "RIT2" "KCNJ16" "CATIP"
## [29] "SPATA2L" "VWA5B1" "SAMD3" "PPP1R36"
## [33] "VAT1L" "NXNL1" "VSTM2B" "POTEG"
## [37] "STARD10" "LINC02869" "RP11-958J22.1" "MTRNR2L1"
## [41] "AF038458.3" "RP5-1015P16.1" "CTD-2201E18.6"
## [1] 2
## [1] "RPH3A" "PDE10A" "PEX5L" "ST6GALNAC5"
## [5] "KIRREL3" "MMP16" "NDST3" "OTOGL"
## [9] "FSTL5" "MTSS1" "HOPX" "ERICH3"
## [13] "CCBE1" "TAFA1" "GRM7" "AP000233.4"
## [17] "MRPS9-AS2" "LINC01266" "RP11-170M17.1" "CCDC26"
## [21] "AC011288.2" "MIR181A1HG" "LINC01036" "AC079807.4"
## [25] "LINC00326" "KIF5C-AS1" "RP1-232L24.3" "LINC01934"
## [29] "CXXC4-AS1" "RP11-410D17.2" "RP11-436F23.1" "RP11-380P13.1"
## [33] "LINC00923" "RP11-586K2.1" "AB015752.3" "RP4-809F18.1"
## [37] "LINC02389" "MTRNR2L8" "CTXND1" "RP11-413N10.3"
## [41] "RP11-57G22.3" "RP11-640F22.1" "RP11-320L2.1" "RP11-120J1.2"
## [45] "KRTAP5-AS1"
## [1] 3
## [1] "SIDT1" "ANKRD7" "LRRC9" "RGS22"
## [5] "PEBP4" "KCTD1" "PLXNC1" "LIX1"
## [9] "SAXO1" "KIF6" "FREM1" "VWA3B"
## [13] "NRG4" "DNAH12" "VWA3A" "LINC01006"
## [17] "ENO4" "HMGN5" "CRPPA" "AC105760.2"
## [21] "LINC01185" "LINC01239" "LINC01695" "RP11-132E11.2"
## [25] "LINC01358" "RP11-624M8.1" "NECTIN3-AS1" "RP11-114J13.1"
## [29] "LINC01340" "LINC02615" "CTB-178M22.2" "RP11-708B6.2"
## [33] "RP11-867G2.8" "RP11-266O8.1" "LINC02326" "RP11-352M15.1"
## [37] "CRTC3-AS1" "RP11-290O12.2" "RP5-847G17.1" "RP11-335E8.3"
## [41] "RP1-84D21.2" "RP11-341N18.1" "RP11-788A4.3" "DISP3"
## [45] "RP11-348F1.3"
## [1] 4
## [1] "LRRC7" "PSD" "SEL1L2" "KIAA1549L"
## [5] "WARS1" "SPOCK1" "PRELID2" "GAS7"
## [9] "SYT7" "KLF6" "TESC" "KLHL4"
## [13] "USP9Y" "MOB3B" "TSHZ3" "QRICH2"
## [17] "DPP6" "COL5A1" "AK7" "ADAM12"
## [21] "CNKSR2" "SEC24D" "COX7A1" "LRRC2"
## [25] "NLGN4Y" "PGM2L1" "DEPP1" "SLC38A11"
## [29] "TPST1" "TTTY14" "CSMD1" "CCK"
## [33] "DPYD" "MEG3" "RP11-513I15.6" "MIR34AHG"
## [37] "SATB1-AS1" "TTTY10" "LINC00278" "IQCM"
## [41] "LINC01322" "PTCHD4" "MIR23AHG"
## [1] 5
## [1] "TMEM241" "RERG" "C2CD6" "ADRA1B"
## [5] "PAH" "GPR39" "NAP1L3" "GRM3"
## [9] "DIO2" "LCNL1" "RP1-292B18.4" "PLCG1-AS1"
## [13] "EPS15-AS1" "AP000282.2" "LINC01344" "RP1-45C12.1"
## [17] "AC007682.1" "RP11-142A5.1" "RBMS3-AS3" "AC079305.11"
## [21] "RP11-154H17.1" "MEF2C-AS2" "HS3ST5" "F11-AS1"
## [25] "LINC01301" "RP1-84O15.2" "LINC00534" "RP11-317N12.1"
## [29] "ZFHX4-AS1" "RP11-431M3.1" "RP11-260G13.1" "RP11-526N18.1"
## [33] "RP11-242P2.1" "RP11-524F11.2" "RP11-103J8.1" "RP11-561I11.4"
## [37] "LINC00540" "LINC01727" "CH17-174L20.1" "RP3-383B8.1"
## [41] "RP11-624A4.2" "RP11-399K19.1" "MEIKIN" "MAFG-DT"
## [1] 6
## [1] "DNASE1L1" "FAR2" "PPEF1" "EPB41L4B" "IQCH" "CEMIP"
## [7] "FRK" "HSD11B1" "EPSTI1" "GULP1" "CCDC102B" "AXDND1"
## [13] "TMEM130" "EPHX4" "SSR4" "KCNIP1" "THSD4" "ARHGAP8"
## [19] "SYN1" "DCN" "ABCA7" "ATP2B3" "CASS4" "CELF4"
## [25] "SUSD1" "CHD5" "SPP1" "DUSP1" "AIF1L" "LOXL1"
## [31] "MICAL1" "DOCK10" "SLC44A5" "SH3GL1" "COL6A2" "FBXO32"
## [37] "ITGA2" "ENOX2" "MAP1A" "NPTX1" "LRRC8C" "CTXN1"
## [43] "MB21D2"
## [1] 7
## [1] "MAP2K6" "ID1" "C4orf45" "RP11-793A3.2" "HGF"
## [6] "RASSF1" "FOSL2" "PPP1R15A" "GADD45B" "RELB"
## [11] "IL1R1" "IGSF21" "ID3" "TBX2" "ITIH5"
## [16] "HELB" "KLF2" "GALNT8" "JUND" "ZSWIM4"
## [21] "IRAK2" "ITPRIP" "SLC43A1" "RASSF3" "RHPN1"
## [26] "ATF3" "NFIL3" "FOS" "JUNB" "PLEKHG5"
## [31] "RND1" "HAP1" "CAVIN1" "CHST6" "MAFF"
## [36] "MITF" "SAMD11" "SLC6A9" "CFI" "S1PR3"
## [41] "RP1-187B23.1" "RP3-365E2.1"
## [1] 8
## [1] "ATP11A" "RASD1"
## [3] "CLIC5" "ELL2"
## [5] "ACAT2" "CRISPLD1"
## [7] "SLC44A3" "SVEP1"
## [9] "PCED1B" "PAPPA"
## [11] "GPC6" "PROS1"
## [13] "F5" "OSMR-AS1"
## [15] "RP11-255O19.2" "VCAN"
## [17] "ST6GAL1" "FRY"
## [19] "PIR" "P3H2"
## [21] "RASL12" "SPAG1"
## [23] "AEBP1" "CCL2"
## [25] "PRRX1" "MAN1C1"
## [27] "SMAD9" "GFPT2"
## [29] "PATJ" "TMTC1"
## [31] "DOCK11" "MYO1E"
## [33] "ARHGEF3" "FBN1"
## [35] "KIF5C" "CLIC4"
## [37] "CXXC5" "SLCO3A1"
## [39] "SPATA13_ENSG00000182957" "NHS"
## [41] "TCEA3" "CTD-2054N24.2"
## [43] "RP11-403A3.3"
## [1] 9
## [1] "USH1C" "CAP2" "BEX2" "MIPOL1" "LMOD1"
## [6] "CES2" "ADAP2" "AQP1" "KLHL13" "MAP3K9"
## [11] "CCDC124" "PDZD4" "PDK3" "TRHDE" "EBF4"
## [16] "TSPAN11" "NRP2" "ASL" "LRRC4B" "TMCC2"
## [21] "CCDC146" "KIAA0513" "TTLL7" "EGF" "CDR2"
## [26] "CCDC40" "MVB12A" "SNTG1" "TBX6" "DEPTOR"
## [31] "C1orf87" "ZMAT4" "REPS2" "MOB3A" "SYT12"
## [36] "PPM1E" "SWI5" "ST8SIA3" "YOD1" "RASGEF1A"
## [41] "NHSL2" "AC004951.6" "ATP6V0D1-DT"
## [1] 10
## [1] "SIPA1L2" "APOC1" "HESX1" "SAMD4A" "HDAC9" "ATP9A"
## [7] "ATP2B4" "CDON" "PDE4A" "PHACTR3" "EEF2K" "SYT17"
## [13] "OLFM2" "SIPA1L3" "ABCC3" "KLHL29" "HIP1" "EDA2R"
## [19] "GFAP" "HAVCR2" "MAPK4" "NFIC" "ENSA" "ITPKB"
## [25] "BOC" "TIAM2" "CNKSR3" "NCAM2" "ARHGAP35" "FBXO27"
## [31] "SLC20A2" "DHRSX" "IFFO2" "NPAS2" "SH3PXD2B" "PACS1"
## [37] "SYNM" "ZBTB7C" "ZFP36L1" "RILPL1" "SRGAP1" "MEF2B"
## [43] "C19orf38"
## [1] 11
## [1] "MSMO1" "YBX3" "NTN1" "SLC39A14" "RPL18A" "RPL19"
## [7] "RPS15" "HS3ST3B1" "RPL36" "RPLP1" "FAU" "PBX3"
## [13] "GLRX" "RPS27" "ZNF48" "RPS18" "CD99" "VRK2"
## [19] "CERS4" "CTCF" "COTL1" "SLC7A5" "KAT8" "PLIN3"
## [25] "KCNN1" "NAMPT" "UST" "ECE1" "RTN2" "RTN3"
## [31] "GLTP" "RTN1" "FSIP1" "FGF17" "ZER1" "PKNOX2"
## [37] "EVA1C" "ZNF608" "PTPN9" "ANO6" "CMTM4"
## [1] 12
## [1] "XK" "CALCRL" "WSCD2" "CCDC80"
## [5] "SLC8A3" "PLCB4" "IFI44L" "HS3ST3A1"
## [9] "CHODL" "ADAMTS9" "GUCY1A1" "WDR97"
## [13] "CYP4F12" "CYP4F3" "CLDN4" "RFX8"
## [17] "STUM" "INSYN2B" "RP11-735G4.1" "LINC01515"
## [21] "LINC01768" "DIRC3" "LINC01725" "DIRC3-AS1"
## [25] "AC007563.5" "LINC02814" "LINC00407" "AC092684.1"
## [29] "SOCS2-AS1" "RP11-364L4.3" "RP11-124B13.1" "MAP1LC3B2"
## [33] "RP11-354K4.2" "LINC00836" "LINC00842" "RP11-364P22.4"
## [37] "RP11-492O8.3" "RP11-96C13.1" "CTD-2040G12.2" "RP11-259G3.1"
## [41] "RP11-154D6.3" "RP11-609L3.3" "RP1-20N4.2" "RP11-423B13.1"
## [45] "LINC02506"
## [1] 13
## [1] "PRKAR2B" "GAB2" "CCDC85A" "ELAVL2" "PPM1H" "MASP1"
## [7] "BTBD11" "CADPS" "ABTB2" "ROBO2" "PLEKHA5" "SYT1"
## [13] "RASAL2" "RBFOX1" "MAST3" "DOK5" "BNIP3L" "SH3PXD2A"
## [19] "ZMIZ1" "CPE" "KIAA1217" "NAV1" "ECE2" "DIAPH2"
## [25] "ZEB1" "ANK3" "MAGI1" "AKAP6" "TIAM1" "SPTBN4"
## [31] "SHANK1" "PLEKHA7" "RBFOX3" "DLGAP1" "DAB1" "CNTNAP2"
## [37] "RGS6" "RALYL" "KCNIP4" "ELAVL3" "ARID5A" "RYR2"
## [1] 14
## [1] "CDH10" "PON3" "DNAH7" "DPH6"
## [5] "MAEL" "HEG1" "TMEM132C" "SLC24A3"
## [9] "HDHD5-AS1" "SULT1A2" "DCHS2" "AC074391.1"
## [13] "SOX1-OT" "POT1-AS1" "PPP1R26-AS1" "AC012593.1"
## [17] "RP11-162D16.2" "SOX21-AS1" "LNC-LBCS" "XIST"
## [21] "PPP1R9A-AS1" "RP11-4B14.3" "LINC00877" "SUCLG2-AS1"
## [25] "RP11-167H9.4" "LINC02144" "RP11-268P4.5" "RP11-284M14.1"
## [29] "LINC00499" "RP11-404I7.2" "GS1-57L11.1" "RP11-541P9.3"
## [33] "RP11-134O21.1" "RMST" "PRANCR" "AC007193.6"
## [37] "CTC-498M16.4" "RP11-378A12.1" "RP4-681L3.3" "RP11-175O15.1"
## [41] "RP11-346I3.7" "RP11-563M4.2" "CTD-2297M2.1" "RP11-215I16.3"
## [1] 15
## [1] "DNAH9" "MAOB" "SEMA3A" "SLC2A9" "SH3D19"
## [6] "PHACTR2" "DPYSL3" "TACR1" "LEPR" "TFAP2E"
## [11] "UBE3D" "ENOX1" "EEPD1" "LYPD6B" "PTH1R"
## [16] "NDUFAF2" "GALNT10" "METTL2B" "DPP10" "GPR156"
## [21] "CA8" "EXT1" "IMMP2L" "SMYD3" "APTR"
## [26] "CTA-292E10.6" "SYNPO2L-AS1" "HSD17B14" "UBE2R2" "ZBTB16"
## [31] "ST8SIA1" "SERPINI2" "PLXDC2" "HIVEP3" "FCHO1"
## [36] "GDPD5" "ZNF704" "WNK2" "LDLRAD4" "STX8"
## [41] "KCND3"
## [1] 16
## [1] "MGAT3" "TACC2" "FAM117B" "FAXC"
## [5] "NXN" "SLC43A2" "LRRN2" "RNLS"
## [9] "LMCD1-AS1" "RP11-390F4.6" "TRMT9B" "CTD-2126E3.6"
## [13] "GTF2IRD1" "EYA2" "RFX2" "PCSK5"
## [17] "MYO9B" "COBL" "RFX4" "WLS"
## [21] "ZC4H2" "TICAM1" "SEM1" "ZBTB46"
## [25] "RFTN1" "RAP1GAP2" "GMPR" "ADAMTS10"
## [29] "GABPB2" "CLVS2" "DENND2A" "CLSTN2"
## [33] "FAM107A" "PIK3CD" "C7orf61" "HRH1"
## [37] "PLCG2" "LYRM4" "KIF9-AS1" "OLMALINC"
## [41] "RP3-414A15.10" "FBXO17"
## [1] 17
## [1] "ANKRD24" "SEZ6L" "MROH8" "CPED1"
## [5] "GABRA4" "DNAH6" "BICC1" "SLC14A1"
## [9] "FHAD1" "ARHGAP18" "SLC22A3" "TEX9"
## [13] "BEND6" "PLEKHG4B" "SPATA17" "CA3"
## [17] "ODAD2" "RNF150" "RNF212" "C9orf153"
## [21] "COL25A1" "IL1RAPL2" "ADD3-AS1" "MT1H"
## [25] "FBXO16" "LINC01876" "RP1-167A14.2" "AC097721.2"
## [29] "PATL2" "RP11-120D5.1" "LINC00886" "RP11-11N9.4"
## [33] "CTC-329D1.2" "RP11-20I20.2" "SPESP1" "ADGRL1-AS1"
## [37] "GEMIN7-AS1" "PLS3-AS1" "APP-DT" "RP11-496B10.6"
## [41] "RP11-314E10.1" "DNAH5" "TEKT1" "NOL4L"
## [45] "LINC00342"
## [1] 18
## [1] "UPP2" "MOGAT1" "TMEM132B" "EFCAB11"
## [5] "KIAA1328" "MAP3K7CL" "C11orf65" "C12orf42"
## [9] "CATSPERE" "LEKR1" "FIRRE" "LIPE-AS1"
## [13] "AC007277.3" "AC004540.5" "LYPLAL1-DT" "LINC01277"
## [17] "RP11-498J9.2" "MMADHC-DT" "RFX3-AS1" "RAP2C-AS1"
## [21] "UFL1-AS1" "RPL34-DT" "NPIPB2" "COX10-AS1"
## [25] "LINC01376" "RP11-550I24.2" "RP11-461O7.1" "RP11-669M16.1"
## [29] "RP11-130F10.1" "LINC01182" "RP11-679C8.2" "MAILR"
## [33] "C8orf37-AS1" "RP11-156K13.1" "LINC02740" "RP11-727A23.10"
## [37] "RP11-20E24.1" "RP11-111A21.1" "CTD-2349P21.11" "RP11-281A20.2"
## [41] "RP11-69G16.2" "RP4-660H19.2" "RP11-168F16.1" "RP5-921G16.1"
## [1] 19
## [1] "RP1-230L10.1" "LINC02715" "TMEM38A" "CATSPERG"
## [5] "CLIP2" "NKD1" "CCDC3" "FAM151B"
## [9] "LMNTD1" "LRGUK" "ST3GAL2" "CFAP251"
## [13] "ORAI2" "ZNF653" "ARMC3" "PDZRN4"
## [17] "C2" "ATOH8" "NWD1" "CFAP54"
## [21] "TOGARAM2" "ODAD4" "NRSN2-AS1" "LINC00884"
## [25] "EPCAM-DT" "HMGA1P4" "RP11-305L7.3" "MIR4300HG"
## [29] "LINC01411" "RP11-279O9.4" "LINC01094" "RP11-507B12.2"
## [33] "RP11-507B12.1" "ZNF594-DT" "KLF2-DT" "CTD-2189E23.1"
## [37] "RP11-35G9.5" "CASTOR2" "RP11-154H23.4" "RP11-514P8.10"
## [41] "RP11-379B18.8" "RP11-114N1.1" "RP11-465L10.14" "RP11-301F14.1"
## [45] "RP11-103P4.1"
## [1] 20
## [1] "SLC26A8" "SNAP25-AS1" "LINC02763" "COL5A3"
## [5] "WFDC1" "XYLT1" "LGR6" "DOC2A"
## [9] "PID1" "MRAS" "ESYT3" "RANBP3L"
## [13] "CHST11" "CSDC2" "MRGPRF" "HPSE2"
## [17] "CALCB" "FZD8" "CTD-2527I21.15" "NME9"
## [21] "ZNF804B" "FLRT2" "NOTUM" "FZD9"
## [25] "AJAP1" "ZNF98" "TMEM184B" "HRAT92"
## [29] "AC064875.2" "HPN-AS1" "AC003991.3" "SPRY4-AS1"
## [33] "AC002127.4" "PDYN-AS1" "AC016745.3" "ETV5"
## [37] "LINC02208" "LINC01414" "LINC01619" "RP11-328J6.1"
## [41] "CEACAM16-AS1" "PKD1L3" "RP11-237N2.1" "RP11-183J19.1"
## [1] 21
## [1] "COL4A2" "RP4-613B23.1" "BAIAP3" "APBA2"
## [5] "TLE2" "ITPKC" "P2RX7" "CDKL1"
## [9] "TUSC3" "FGL1" "CHRNE" "ARSB"
## [13] "PADI2" "COL21A1" "PRR12" "PTPRE"
## [17] "PLCE1" "RHBDL3" "ADCY8" "SLC5A11"
## [21] "TMCO4" "SHISA5" "EDIL3" "ELAPOR2"
## [25] "TMC1" "GPR176" "NPNT" "LINGO1"
## [29] "SLC26A5" "FRMD3" "GPR137C" "SPACA6"
## [33] "TSHZ2" "UTY" "DMWD" "COL27A1"
## [37] "LINC00685" "RP5-864K19.4" "RP5-1198O20.4" "L3MBTL2-AS1"
## [41] "KCNK15-AS1" "RP3-466I7.2"
## [1] 22
## [1] "PRKCQ" "EPHA6" "SCG3" "EPM2A" "GBE1" "EPHA4"
## [7] "PPP1R3C" "CCDC59" "C10orf90" "TSPAN5" "SNTB1" "STOX2"
## [13] "ROR1" "KLHL32" "SHISA6" "VKORC1L1" "TENM3" "MRPL33"
## [19] "ITGA3" "COL23A1" "MCF2L2" "SYNE2" "CAMK2B" "TBC1D1"
## [25] "RARB" "DNM1" "PPARGC1A" "DMGDH" "VAV3" "CCNH"
## [31] "TNS3" "SDK1" "DGKZ" "ABCB9" "THRB" "RFTN2"
## [37] "ALK" "ABAT" "EFNA5" "PARVA" "DNM3"
## [1] 23
## [1] "RP11-104E19.1" "USH2A"
## [3] "LAMB4" "SLC26A3"
## [5] "STEAP1B" "BEST3"
## [7] "SCN2A" "CBLN2"
## [9] "SLC4A10" "CDH18"
## [11] "ZNF385D" "SLC24A2"
## [13] "GREM1" "HTR1E"
## [15] "SEMA3E" "KCNH7"
## [17] "CACNA1E" "MMP17"
## [19] "AC023469.1" "RP11-191L9.4"
## [21] "RP1-35C21.2" "RP11-147G16.1"
## [23] "RP11-154D17.1" "RP5-827C21.2"
## [25] "SHISA9" "AC002066.1"
## [27] "CTC-340A15.2" "RP11-384F7.1"
## [29] "RP11-17A1.3" "RP11-446J8.1"
## [31] "RP11-26J3.1" "LINC02742"
## [33] "LINC01609" "RP11-20D14.3"
## [35] "RP11-499F3.2" "LINC00558"
## [37] "MTRNR2L12" "RMRP_ENSG00000269900"
## [39] "SCARNA2_ENSG00000270066" "CH507-513H4.1"
## [41] "CH507-528H12.1" "RP4-799O8.1"
## [43] "AC003099.2" "RP11-398J12.1"
## [45] "RP11-4D11.1"
## [1] 24
## [1] "NID1" "F3" "MT1G" "MTERF1"
## [5] "PUDP" "AGBL3" "MN1" "MT1E"
## [9] "SGCD" "MACROD2" "CYP7B1" "DLEU1"
## [13] "CC2D2B" "COL28A1" "AC072062.3" "Z83001.1"
## [17] "HDAC2-AS2" "RP11-154D6.1" "OBI1-AS1" "RNF217-AS1"
## [21] "PTPRG-AS1" "SOX2-OT" "RP11-373N22.3" "LINC00504"
## [25] "LINC01950" "RP11-582J16.4" "LIX1-AS1" "RP11-673E1.1"
## [29] "LINC02328" "AC004158.3" "LINC01572" "RP11-436D23.1"
## [33] "LINC02664" "RP11-470M1.2" "RP11-437L7.2" "RP11-692P14.1"
## [37] "RP11-1289C17.1" "RP11-520F22.1" "UNC5B" "TGIF2"
## [41] "TENM2" "FAXDC2" "KBTBD12" "LINC01252"
## [1] 25
## [1] "NRXN3" "ZFR2" "RGS4" "UNC13A" "CALY"
## [6] "TESPA1" "PLK2" "MLIP" "LRRIQ3" "ANKRD33B"
## [11] "GRIK2" "NEGR1" "GALNTL6" "RGS7" "KCTD16"
## [16] "CCSER1" "STAC3" "PCLO" "SLIT1" "ERC2"
## [21] "DLGAP2" "PWRN1" "RIMS1" "ATRNL1" "KHDRBS2"
## [26] "PDE1A" "RIMS3" "ZNF385B" "CNTN5" "GRM5"
## [31] "NLGN1" "FRMPD4" "ARPP21" "NABP1" "RIMS2"
## [36] "SAMD12" "OPCML" "SYN3" "KCNQ5" "PTPRT"
## [41] "RP1-30E17.2" "PCAT1"
## [1] 26
## [1] "STK32A" "BNC2" "RP11-116N8.1" "ST6GALNAC2"
## [5] "FAP" "SLCO1A2" "JHY" "SOHLH2"
## [9] "LRAT" "TTC9" "SCN1A" "HNMT"
## [13] "CCDC175" "PARP8" "ANGPT1" "GAL3ST2"
## [17] "DRC1" "NFASC" "CFAP47" "SLITRK5"
## [21] "COL24A1" "PRIMA1" "PLCXD3" "OVCH1"
## [25] "LAMA2" "AC003090.1" "AC092155.4" "RP11-69I8.3"
## [29] "RP1-111D6.3" "RP11-469A15.2" "RP11-146I2.1" "RP11-90C4.1"
## [33] "AL163953.3" "CTD-2643I7.5" "RP11-190P13.2" "LINC01088"
## [37] "CTB-35F21.1" "LINC00609" "LINC02251" "RP11-259K15.2"
## [41] "RP11-627D16.1" "RP11-210M15.2" "RP11-876N24.2" "RP1-79C4.4"
## [45] "RP11-6L16.1"
## [1] 27
## [1] "CD38" "SP140" "SPATA6L" "PAPPA2"
## [5] "RNF175" "DNAAF1" "PKD1L1" "STPG2"
## [9] "SCN11A" "ZBTB44-DT" "CASC2" "RFLNA"
## [13] "RHCE" "SCOC-AS1" "COL5A2" "MALRD1"
## [17] "CHL1-AS2" "AP001628.6" "TARID" "AC008269.2"
## [21] "ZRANB2-AS2" "LINC00271" "LINC01524" "RP11-195C7.1"
## [25] "LINC01829" "LEFTY1" "DRAIC" "CTB-161M19.4"
## [29] "RP11-1252I4.2" "RP4-785G19.5" "CTC-347C20.1" "LINC02320"
## [33] "RP11-739G5.1" "RP11-525K10.3" "DISC1FP1" "RP11-396B14.2"
## [37] "RP11-397A16.1" "AC005786.7" "RP11-157E16.1" "LINC00506"
## [41] "RP11-964E11.3" "RP11-274G22.1" "RP11-382N13.7" "RP11-444C24.1"
## [45] "RP5-892C22.1"
## [1] 28
## [1] "CTD-2313D3.2" "ADGRL1" "SEC14L5"
## [4] "DGKB" "UNC13C" "ST18"
## [7] "PLCL2" "CFAP161" "SYTL3"
## [10] "ADCY1" "TVP23A" "GSG1L"
## [13] "RCAN2" "PPP1R42" "SLC8A1"
## [16] "OSBP2" "FAM174B" "RTN4RL1"
## [19] "CCDC30" "PDE2A" "SHTN1"
## [22] "PAX8-AS1" "LINC00632" "TNFRSF25"
## [25] "AP001347.6" "XXbac-BPG55C20.7" "TSBP1-AS1"
## [28] "RP11-563D10.1" "LINC01320" "WARS2-AS1"
## [31] "CYP1B1-AS1" "AC067956.1" "LINC02223"
## [34] "RP11-79E3.2" "RP11-624C23.1" "LINC02356"
## [37] "RP11-148E17.1" "RPPH1_ENSG00000259001" "RP11-838N2.5"
## [40] "DGCR5_ENSG00000273032" "SPANXA2-OT1" "RP11-596C23.6"
## [43] "IQCJ-SCHIP1" "RP11-114N19.3" "RP1-166D18.1"
## [1] 29
## [1] "MTCL1" "LINC02884" "ARHGAP31" "DGKG"
## [5] "KIF3C" "MYOM1" "CAB39L" "AGFG2"
## [9] "LGI1" "RIPOR2" "TFDP2" "PDZRN3"
## [13] "TOX2" "HIF3A" "SYNE1" "IQCA1"
## [17] "RIN2" "SHROOM3" "FAM171A1" "FAM13C"
## [21] "CNNM2" "GRIK4" "AHCYL2" "DHRS3"
## [25] "GNG4" "ZFPM2" "FAM222B" "TCAP"
## [29] "IQCK" "PHYHD1" "NCKAP5" "SLC25A20"
## [33] "APOLD1" "ARL15" "TPCN1" "TRPV1"
## [37] "ZNF785" "TOX" "EFCAB2" "HAUS7"
## [41] "LINC01135" "AGBL1" "RP11-799O21.2"
## [1] 30
## [1] "ARHGAP44" "HHAT" "SDK2" "STS"
## [5] "WNT5B" "TENT5A" "PLAGL1" "GTDC1"
## [9] "UNC79" "PKIB" "ARSG" "SUMF1"
## [13] "TMEM108" "ACSL1" "SLC9B1" "ALDH1A1"
## [17] "JAM3" "ANO5" "PNMA3" "KIAA0825"
## [21] "MAML3" "BRINP2" "MAMDC2-AS1" "RP11-306O13.1"
## [25] "LINC00571" "AC026188.1" "LINC01937" "PKN2-AS1"
## [29] "H2AZ1-DT" "LINC02355" "RP11-804N13.1" "MPPED2-AS1"
## [33] "RP11-624D11.2" "RP11-511B23.2" "RP11-72M17.1" "RP11-798K3.2"
## [37] "IDH2-DT" "PSMD7-DT" "LINC00907" "TSIX"
## [41] "CTC-490G23.6" "RP11-221G19.1" "CPM"
## [1] 31
## [1] "MRC2" "FAM107B" "REEP1" "KCNN2"
## [5] "SGK2" "RIPK2" "NT5DC3" "B3GAT2"
## [9] "WIPF1" "ADCY7" "IFI6" "TRIM5"
## [13] "EPHB2" "AVIL" "ARRDC4" "LPAR4"
## [17] "MON1A" "FABP5" "PRTG" "SCG5"
## [21] "C1QTNF4" "GINS3" "PIWIL2" "L3MBTL3"
## [25] "SAMD13" "HLA-E" "LGALSL-DT" "LRRC24"
## [29] "RP11-373E16.6" "ARHGAP6" "ADAP1" "CLSTN3"
## [33] "TMEM200A" "NT5DC2" "SPSB1" "PAWR"
## [37] "FAM110C" "OSTN" "AC013463.2" "CRYBB2"
## [41] "RP11-542F9.2" "RP11-93B21.2"
## [1] 32
## [1] "MBNL3" "MT3" "SRPX" "IL7"
## [5] "PSG8" "APOE" "TMEM160" "EMP1"
## [9] "PDE5A" "ABCA12" "HMGA2" "GFRA1"
## [13] "DLC1" "LRRC3B" "PLD5" "MT1X"
## [17] "PTMA" "EYS" "KCNMB2" "HES5"
## [21] "RANBP17" "ANKUB1" "AC009501.4" "GNG12-AS1"
## [25] "RP5-1101C3.1" "LUCAT1" "CTD-2015H6.3" "VCAN-AS1"
## [29] "RP11-517I3.1" "ZFPM2-AS1" "RP11-649G15.2" "CTD-2537O9.1"
## [33] "PTCSC3" "RHOBTB1" "ARID3A" "FREM2"
## [37] "PTMS" "OXR1" "CKB" "CRADD"
## [41] "PDE3A" "ZMAT3" "DUSP8"
## [1] 33
## [1] "LINC01931" "HHIP" "CLMP" "GLIPR1L1"
## [5] "P2RY14" "SGCZ" "FSIP2" "RNF212B"
## [9] "HEPN1" "AC002463.3" "RP11-131L23.1" "RP4-660H19.1"
## [13] "RP11-547I7.1" "ST7-AS2" "PCDH9-AS2" "GPC5-AS2"
## [17] "GRM3-AS1" "PCDH9-AS4" "RP11-109I13.2" "LINC02250"
## [21] "AC008067.2" "RP11-475C16.2" "RP13-143G15.4" "LINC02877"
## [25] "RP11-657O9.1" "ZBTB20-AS5" "LINC00960" "GK-AS1"
## [29] "RP11-115N4.1" "RORA-AS1" "LRP4-AS1" "MAPK10-AS1"
## [33] "RP11-116O11.1" "STPG2-AS1" "RP11-351A11.1" "RP11-463D19.1"
## [37] "AP000462.2" "RP11-370I10.2" "LINC01579" "DIO2-AS1"
## [41] "RP11-39M21.1" "CTD-2282P23.2" "RP11-576O3.1" "RP11-394G3.3"
## [45] "RP11-66G15.1"
## [1] 34
## [1] "IDI1" "BLVRB" "PLS3" "SLC1A2" "GMDS"
## [6] "MT2A" "CABLES1" "PRR5L" "C4orf19" "ABHD3"
## [11] "CMSS1" "MALAT1" "SESN1" "PALM" "DAAM1"
## [16] "CDH20" "ARHGEF18" "CPEB3" "TANC1" "C1orf21"
## [21] "ZFP36" "ZSWIM6" "ADGRB3" "ARHGAP29" "JAZF1"
## [26] "GNA14" "NRG2" "PTCHD1" "CACNB2" "NAV2"
## [31] "PCDH7" "CADM2" "GNG7" "LDLRAD3" "FIGN"
## [36] "LHFPL6" "MAML2" "CPEB1" "LINC00511" "DLEU2"
## [41] "PTCHD1-AS" "TMEM161B-AS1"
## [1] 35
## [1] "RRAGD" "AHRR" "BCAS1" "ARHGAP28"
## [5] "SLC16A6" "TRIM22" "FHDC1" "DUSP15"
## [9] "RETREG1" "GFRA2" "DELEC1" "SNX31"
## [13] "CIITA" "CYP4X1" "IER5L" "NPSR1-AS1"
## [17] "LINC01117" "LINC01630" "RP1-223B1.1" "LINC01503"
## [21] "AC009264.1" "MSC-AS1" "PRKAR2B-AS1" "LINC02217"
## [25] "LINC01618" "LINC00958" "RP11-745L13.2" "CENATAC-DT"
## [29] "LINC02327" "LINC00637" "LINC02254" "MAPT-AS1"
## [33] "RP1-41C23.1" "RP11-355F16.1" "RP11-323P17.2" "PRAG1"
## [37] "RP5-965G21.3" "LINC01374" "RP11-239A17.1" "CTC-428H11.2"
## [41] "RP11-313M3.2" "AC006296.4" "MCUB" "PLPP4"
## [45] "RP11-403A3.2"
## [1] 36
## [1] "CD200R1" "GRK3" "TFCP2L1" "ACVR1C"
## [5] "LRMDA" "KCNE4" "TDRD9" "SHROOM4"
## [9] "FAAH2" "METTL7B" "SLC25A18" "PLK5"
## [13] "TRDN" "NKAIN2" "C3orf35" "LINC00862"
## [17] "PLIN5" "RP11-174G6.1" "AP000318.2" "LINC00598"
## [21] "ARL17B" "AC104088.1" "LINC01137" "KCNMB2-AS1"
## [25] "ARHGEF26-AS1" "RTL9" "ALDH1L1-AS2" "STX18-AS1"
## [29] "DPH6-DT" "LINC02315" "RP11-346L1.2" "RP11-298I3.1"
## [33] "RP11-150C16.1" "CASC17" "RP1-158P9.2" "TAPT1-AS1"
## [37] "RP11-60A24.3" "AC079610.1" "RP11-711K1.8" "LINC02246"
## [41] "RP11-26L21.1" "RP11-166M16.1" "RP11-404C6.6" "RP11-125C10.1"
## [1] 37
## [1] "MAMLD1" "SNCAIP" "PNPLA3" "GALNT16"
## [5] "LAMA4" "SLC24A4" "SYCP2L" "ABI3BP"
## [9] "HNF4G" "SUGCT" "SLC4A5" "LINC02649"
## [13] "RP11-344B5.2" "SNHG31" "AF131217.1" "LINC02652"
## [17] "LINC02234" "NEUROG2-AS1" "MGAM" "FRMD6-AS2"
## [21] "RP11-571L19.7" "RP11-574F11.4" "NIPAL3" "CNTN1"
## [25] "ATP1A2" "RNF19A" "RNF24" "PPP1R13L"
## [29] "B4GALT2" "NCAN" "SLC39A11" "ARHGEF4"
## [33] "BCAS3" "KCNN3" "SEMA3D" "PDPN"
## [37] "ABCA1" "FAT3" "SLC35E3" "RGMA"
## [41] "CNTN2" "TMEM229B" "EML6"
## [1] 38
## [1] "ASB4" "TENM1" "MYO16" "TRPM3" "ID2" "BEX1"
## [7] "CD72" "CXCL14" "IGFBP7" "ALCAM" "RIMBP2" "CTNNA2"
## [13] "ISYNA1" "GLIS3" "CLNK" "LIN7A" "TPD52L1" "CCND3"
## [19] "CTSD" "STAG1" "FOXO3" "TEX11" "MACF1" "PALLD"
## [25] "SOX5" "SSH2" "PAM" "ARHGAP26" "FOXO1" "DST"
## [31] "MGAT5" "ART3" "C2CD2" "ABR" "PFKFB3" "FRMD5"
## [37] "MYO1D" "LSMEM2" "CADM1" "PCP4" "IRS2" "NEAT1"
## [1] 39
## [1] "CA1" "WDR64" "SHOC1" "FILIP1L"
## [5] "SEPTIN1" "TSBP1" "TMLHE-AS1" "AC105461.1"
## [9] "AC017101.10" "ASTN2-AS1" "RP11-141A19.1" "RP11-417B4.2"
## [13] "GNA14-AS1" "RP11-46O21.2" "LINC00513" "AC037445.1"
## [17] "STARD13-AS" "GS1-433O24.1" "LINC01877" "RP11-768G7.3"
## [21] "RP11-274H2.2" "ANK2-AS1" "RP11-223C24.1" "RP11-348J24.1"
## [25] "RP11-120A1.1" "RP11-39E3.3" "CTD-3239E11.2" "BBOX1-AS1"
## [29] "RP11-1H15.2" "RP11-513G19.1" "A2ML1-AS1" "RP11-315E17.1"
## [33] "RP11-887P2.5" "RP11-184D12.1" "CRIM1-DT" "RP11-58G13.1"
## [37] "RP11-138H11.1" "RP11-80I3.1" "CH17-140K24.2" "RP11-793H13.14"
## [41] "CTD-2172F7.1" "RP11-555K12.4" "DNAH11" "ZNF208"
## [45] "LINC01208"
## [1] 40
## [1] "ANOS1" "PCSK1N" "SRPX2" "POLR2I"
## [5] "PDE8B" "GDAP1L1" "H3-3B" "ITGA9"
## [9] "LRTM1" "CHST9" "MEGF11" "BTG2"
## [13] "MFSD4B" "HES4" "CARNMT1-AS1" "RP11-106M7.1"
## [17] "DPP10-AS3" "IPO9-AS1" "RP11-666F17.1" "DPP10-AS1"
## [21] "RP11-446H18.5" "CDKN2B-AS1" "BAALC-AS1" "SEMA6A-AS1"
## [25] "C1QTNF7-AS1" "RP11-711G10.1" "RP11-157I4.4" "RP11-452H21.1"
## [29] "AP000487.6" "RP11-144F15.1" "RP11-363J20.2" "HIF1A-AS3"
## [33] "PRKCA-AS1" "CTC-513N18.6" "ARRDC3-AS1" "SLC7A14-AS1"
## [37] "RP11-589M4.5" "BCL6-AS1" "RP11-125D12.3" "RP11-725F23.1"
## [41] "RP11-592G13.2" "RP11-875G18.1" "NUP210L"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_7"
## [1] "MAP2K6" "ID1" "C4orf45" "RP11-793A3.2" "HGF"
## [6] "RASSF1" "FOSL2" "PPP1R15A" "GADD45B" "RELB"
## [11] "IL1R1" "IGSF21" "ID3" "TBX2" "ITIH5"
## [16] "HELB" "KLF2" "GALNT8" "JUND" "ZSWIM4"
## [21] "IRAK2" "ITPRIP" "SLC43A1" "RASSF3" "RHPN1"
## [26] "ATF3" "NFIL3" "FOS" "JUNB" "PLEKHG5"
## [31] "RND1" "HAP1" "CAVIN1" "CHST6" "MAFF"
## [36] "MITF" "SAMD11" "SLC6A9" "CFI" "S1PR3"
## [41] "RP1-187B23.1" "RP3-365E2.1"
## $reactome
## category
## 604 ngf stimulated transcription
## 626 nuclear events kinase and transcription factor activation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 604 5.323741e-06 0.9999999 5 10
## 626 1.113843e-05 0.9999997 5 13
## FDR
## 604 0.005978561
## 626 0.006254226
##
## [1] "set_11"
## [1] "MSMO1" "YBX3" "NTN1" "SLC39A14" "RPL18A" "RPL19"
## [7] "RPS15" "HS3ST3B1" "RPL36" "RPLP1" "FAU" "PBX3"
## [13] "GLRX" "RPS27" "ZNF48" "RPS18" "CD99" "VRK2"
## [19] "CERS4" "CTCF" "COTL1" "SLC7A5" "KAT8" "PLIN3"
## [25] "KCNN1" "NAMPT" "UST" "ECE1" "RTN2" "RTN3"
## [31] "GLTP" "RTN1" "FSIP1" "FGF17" "ZER1" "PKNOX2"
## [37] "EVA1C" "ZNF608" "PTPN9" "ANO6" "CMTM4"
## $reactome
## category
## 287 eukaryotic translation elongation
## 288 eukaryotic translation initiation
## 610 nonsense mediated decay nmd
## 810 response of eif2ak4 gcn2 to amino acid deficiency
## 878 selenoamino acid metabolism
## 856 rrna processing
## 975 srp dependent cotranslational protein targeting to membrane
## 429 influenza infection
## 527 metabolism of amino acids and derivatives
## 1078 translation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 287 2.244375e-11 1 8 9
## 288 2.244375e-11 1 8 9
## 610 2.244375e-11 1 8 9
## 810 6.683496e-11 1 8 10
## 878 1.149188e-10 1 8 10
## 856 1.296637e-10 1 8 10
## 975 3.310714e-10 1 8 11
## 429 3.400822e-10 1 8 11
## 527 1.623451e-09 1 9 17
## 1078 2.813057e-09 1 8 13
## FDR
## 287 8.401445e-09
## 288 8.401445e-09
## 610 8.401445e-09
## 810 1.876391e-08
## 878 2.426873e-08
## 856 2.426873e-08
## 975 4.773904e-08
## 429 4.773904e-08
## 527 2.025706e-07
## 1078 3.159063e-07
##
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 618 cytoplasmic translation 0 1
## numDEInCat numInCat FDR
## 618 9 12 0
##
## [1] "set_25"
## [1] "NRXN3" "ZFR2" "RGS4" "UNC13A" "CALY"
## [6] "TESPA1" "PLK2" "MLIP" "LRRIQ3" "ANKRD33B"
## [11] "GRIK2" "NEGR1" "GALNTL6" "RGS7" "KCTD16"
## [16] "CCSER1" "STAC3" "PCLO" "SLIT1" "ERC2"
## [21] "DLGAP2" "PWRN1" "RIMS1" "ATRNL1" "KHDRBS2"
## [26] "PDE1A" "RIMS3" "ZNF385B" "CNTN5" "GRM5"
## [31] "NLGN1" "FRMPD4" "ARPP21" "NABP1" "RIMS2"
## [36] "SAMD12" "OPCML" "SYN3" "KCNQ5" "PTPRT"
## [41] "RP1-30E17.2" "PCAT1"
## $go_bp
## category
## 4455 vesicle mediated transport in synapse
## 2093 neurotransmitter secretion
## 4266 synaptic vesicle exocytosis
## 2094 neurotransmitter transport
## 3799 regulation of trans synaptic signaling
## 3060 regulated exocytosis
## 3767 regulation of synaptic vesicle exocytosis
## 3536 regulation of nervous system process
## 270 calcium ion regulated exocytosis of neurotransmitter
## 1526 modulation of excitatory postsynaptic potential
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4455 2.416393e-08 1.0000000 9 29
## 2093 5.700493e-08 1.0000000 8 22
## 4266 8.980176e-08 1.0000000 7 16
## 2094 3.785703e-07 1.0000000 8 29
## 3799 2.697985e-06 0.9999997 12 97
## 3060 3.991929e-06 0.9999998 7 26
## 3767 7.653032e-06 0.9999999 4 6
## 3536 1.322354e-05 0.9999993 6 22
## 270 1.861953e-05 0.9999997 4 7
## 1526 2.521921e-05 0.9999990 5 15
## FDR
## 4455 0.0001084961
## 2093 0.0001279761
## 4266 0.0001344033
## 2094 0.0004249452
## 3799 0.0024227903
## 3060 0.0029872936
## 3767 0.0049088735
## 3536 0.0074217120
## 270 0.0092890748
## 1526 0.0113234270
##
## [1] "set_30"
## [1] "ARHGAP44" "HHAT" "SDK2" "STS"
## [5] "WNT5B" "TENT5A" "PLAGL1" "GTDC1"
## [9] "UNC79" "PKIB" "ARSG" "SUMF1"
## [13] "TMEM108" "ACSL1" "SLC9B1" "ALDH1A1"
## [17] "JAM3" "ANO5" "PNMA3" "KIAA0825"
## [21] "MAML3" "BRINP2" "MAMDC2-AS1" "RP11-306O13.1"
## [25] "LINC00571" "AC026188.1" "LINC01937" "PKN2-AS1"
## [29] "H2AZ1-DT" "LINC02355" "RP11-804N13.1" "MPPED2-AS1"
## [33] "RP11-624D11.2" "RP11-511B23.2" "RP11-72M17.1" "RP11-798K3.2"
## [37] "IDH2-DT" "PSMD7-DT" "LINC00907" "TSIX"
## [41] "CTC-490G23.6" "RP11-221G19.1" "CPM"
## $reactome
## category over_represented_pvalue
## 383 glycosphingolipid catabolism 3.379057e-05
## 1019 the activation of arylsulfatases 3.379057e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 383 0.9999998 3 4 0.01897341
## 1019 0.9999998 3 4 0.01897341
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8954997 478.3 16112782 860.6 NA 15638910 835.3
## Vcells 16666141 127.2 31262822 238.6 65536 31262822 238.6
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] goseq_1.50.0 geneLenDataBase_1.34.0 BiasedUrn_2.0.10
## [4] fgsea_1.24.0 biomaRt_2.54.1 limma_3.54.2
## [7] tidyr_1.3.0 ggpubr_0.6.0 ggplot2_3.4.2
## [10] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 GenomeInfoDb_1.34.9
## [9] tools_4.2.3 backports_1.4.1
## [11] bslib_0.4.2 utf8_1.2.3
## [13] R6_2.5.1 mgcv_1.8-42
## [15] DBI_1.1.3 BiocGenerics_0.44.0
## [17] colorspace_2.1-0 withr_2.5.0
## [19] tidyselect_1.2.0 prettyunits_1.1.1
## [21] bit_4.0.5 curl_5.0.1
## [23] compiler_4.2.3 cli_3.6.1
## [25] Biobase_2.58.0 xml2_1.3.4
## [27] DelayedArray_0.24.0 rtracklayer_1.58.0
## [29] sass_0.4.5 scales_1.2.1
## [31] rappdirs_0.3.3 Rsamtools_2.14.0
## [33] stringr_1.5.0 digest_0.6.31
## [35] rmarkdown_2.21 XVector_0.38.0
## [37] pkgconfig_2.0.3 htmltools_0.5.5
## [39] MatrixGenerics_1.10.0 dbplyr_2.3.2
## [41] fastmap_1.1.1 rlang_1.1.0
## [43] rstudioapi_0.14 RSQLite_2.3.1
## [45] BiocIO_1.8.0 jquerylib_0.1.4
## [47] generics_0.1.3 jsonlite_1.8.4
## [49] BiocParallel_1.32.6 dplyr_1.1.2
## [51] car_3.1-2 RCurl_1.98-1.12
## [53] magrittr_2.0.3 GO.db_3.16.0
## [55] GenomeInfoDbData_1.2.9 Matrix_1.6-4
## [57] Rcpp_1.0.10 munsell_0.5.0
## [59] S4Vectors_0.36.2 fansi_1.0.4
## [61] abind_1.4-5 lifecycle_1.0.3
## [63] stringi_1.7.12 yaml_2.3.7
## [65] carData_3.0-5 SummarizedExperiment_1.28.0
## [67] zlibbioc_1.44.0 org.Hs.eg.db_3.16.0
## [69] BiocFileCache_2.6.1 grid_4.2.3
## [71] blob_1.2.4 parallel_4.2.3
## [73] crayon_1.5.2 lattice_0.20-45
## [75] splines_4.2.3 Biostrings_2.66.0
## [77] cowplot_1.1.1 GenomicFeatures_1.50.4
## [79] hms_1.1.3 KEGGREST_1.38.0
## [81] knitr_1.44 pillar_1.9.0
## [83] GenomicRanges_1.50.2 rjson_0.2.21
## [85] ggsignif_0.6.4 codetools_0.2-19
## [87] stats4_4.2.3 fastmatch_1.1-3
## [89] XML_3.99-0.14 glue_1.6.2
## [91] evaluate_0.20 png_0.1-8
## [93] vctrs_0.6.2 gtable_0.3.3
## [95] purrr_1.0.1 cachem_1.0.7
## [97] xfun_0.39 broom_1.0.4
## [99] restfulr_0.0.15 rstatix_0.7.2
## [101] tibble_3.2.1 GenomicAlignments_1.34.1
## [103] AnnotationDbi_1.60.2 memoise_2.0.1
## [105] IRanges_2.32.0